LAMMPS (8 Apr 2021)
  using 1 OpenMP thread(s) per MPI task
# 3D overdamped active brownian dynamics with no interactions

variable        gamma_t string 3.0
variable        gamma_r string 1.0
variable        temp string 1.0
variable        seed equal 1974019
variable        fp string 4.0
variable        params string ${temp}_${gamma_t}_${gamma_r}_${fp}
variable        params string 1.0_${gamma_t}_${gamma_r}_${fp}
variable        params string 1.0_3.0_${gamma_r}_${fp}
variable        params string 1.0_3.0_1.0_${fp}
variable        params string 1.0_3.0_1.0_4.0

units           lj
atom_style      hybrid dipole sphere
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
dimension       3
newton off

lattice         sc 0.4
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
region          box block -8 8 -8 8 -8 8
create_box      1 box
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
  2 by 1 by 2 MPI processor grid
create_atoms    1 box
Created 4096 atoms
  create_atoms CPU = 0.002 seconds
mass            * 1.0
set             type  * dipole/random ${seed} 1.0
set             type  * dipole/random 1974019 1.0
Setting atom values ...
  4096 settings made for dipole/random
velocity        all create 1.0 1 loop geom

pair_style none

# overdamped brownian dynamics time-step
fix         step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix         step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
fix         step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
fix         step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
fix         step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
# self-propulsion force along the dipole direction
fix         activity all propel/self dipole ${fp}
fix         activity all propel/self dipole 4.0

compute press all pressure NULL virial

thermo_style    custom step ke pe c_press

#equilibration
timestep        0.0000000001
thermo          100
run             5000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes
Step KinEng PotEng c_press 
       0    1.4996338            0  0.068021726 
     100 5.2484581e+09            0  0.068010768 
     200 5.277936e+09            0  0.068024039 
     300 5.2651427e+09            0  0.068014821 
     400 5.2066432e+09            0  0.068027583 
     500 5.2250276e+09            0  0.068030242 
     600 5.239771e+09            0  0.068018406 
     700 5.1953674e+09            0  0.068017081 
     800 5.2097107e+09            0  0.068010167 
     900 5.2559863e+09            0  0.068012923 
    1000 5.2743197e+09            0  0.068017855 
    1100 5.1999741e+09            0  0.068014189 
    1200 5.3216344e+09            0  0.068005604 
    1300 5.2839264e+09            0  0.067982558 
    1400 5.2462761e+09            0  0.067977843 
    1500 5.2208208e+09            0  0.067979594 
    1600 5.2740284e+09            0  0.067972573 
    1700 5.1919692e+09            0  0.067974452 
    1800 5.2497614e+09            0  0.067966417 
    1900 5.2910442e+09            0  0.067976096 
    2000  5.27238e+09            0  0.067963979 
    2100 5.3305398e+09            0   0.06795661 
    2200 5.205471e+09            0  0.067970212 
    2300 5.1803713e+09            0  0.067931775 
    2400 5.2134311e+09            0  0.067941825 
    2500 5.2367424e+09            0  0.067963456 
    2600 5.2246738e+09            0  0.067957556 
    2700 5.2514573e+09            0  0.067960724 
    2800 5.2601577e+09            0  0.067965167 
    2900 5.2422855e+09            0  0.067956561 
    3000 5.1796674e+09            0  0.067946764 
    3100 5.2308189e+09            0  0.067946585 
    3200 5.1835395e+09            0  0.067951909 
    3300 5.2762112e+09            0  0.067963199 
    3400 5.3224133e+09            0  0.067944918 
    3500 5.2314242e+09            0   0.06795318 
    3600 5.2760337e+09            0  0.067958005 
    3700 5.2549349e+09            0   0.06795228 
    3800 5.3343065e+09            0  0.067944561 
    3900 5.2440993e+09            0  0.067947433 
    4000 5.2565026e+09            0  0.067962624 
    4100 5.1766738e+09            0  0.067949542 
    4200 5.2058437e+09            0  0.067959946 
    4300 5.2777775e+09            0  0.067945883 
    4400 5.2020331e+09            0  0.067953495 
    4500 5.1417619e+09            0  0.067944161 
    4600 5.2672994e+09            0  0.067936777 
    4700 5.222847e+09            0  0.067943025 
    4800 5.2467842e+09            0   0.06794191 
    4900 5.2784378e+09            0  0.067939495 
    5000 5.2563969e+09            0  0.067940246 
Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms

Performance: 0.028 tau/day, 3208.260 timesteps/s
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.15304    | 0.15677    | 0.16459    |   1.2 | 10.06
Output  | 0.0012078  | 0.0021182  | 0.0047011  |   3.2 |  0.14
Modify  | 1.1966     | 1.2236     | 1.2761     |   2.8 | 78.51
Other   |            | 0.176      |            |       | 11.29

Nlocal:        1024.00 ave        1024 max        1024 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:        353.000 ave         353 max         353 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep  0

# MSD to demonstrate expected diffusive behaviour for ideal active
# brownian motion, which is
#
#      MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
#            + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
#
# with d being simulation dimension
compute         msd  all msd

thermo_style    custom step ke pe c_msd[*] c_press


timestep        0.00001
thermo          1000

# main run
run             12000
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press 
       0 5.2563969e+09            0            0            0            0            0  0.067940246 
    1000    52568.549            0 0.0067249858 0.0066478843 0.0066014231  0.019974293  0.066777589 
    2000    52836.937            0  0.013611101  0.013799663  0.013161144  0.040571907  0.066769693 
    3000    52129.467            0  0.020360834   0.02089829   0.01995025  0.061209374  0.060026879 
    4000    52075.177            0  0.027638751  0.028062314  0.026895904  0.082596969  0.078290387 
    5000    52203.996            0  0.034087112  0.034933104  0.033832559   0.10285278  0.083657551 
    6000    52986.764            0  0.041562413  0.042238976  0.040542538   0.12434393   0.11542014 
    7000    51941.229            0  0.049216989  0.049250201  0.047598008    0.1460652   0.13739893 
    8000    52618.713            0  0.057198947  0.057409217   0.05404895   0.16865711   0.13681938 
    9000    52501.332            0  0.066447829  0.065262287  0.062271789   0.19398191   0.14306596 
   10000    52545.628            0  0.073800792  0.072510553  0.070100713   0.21641206   0.14689578 
   11000    52416.561            0  0.081881868  0.080638809  0.078969817   0.24149049   0.15608324 
   12000    52271.578            0  0.090521937  0.088555992   0.08592156   0.26499949    0.1474981 
Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms

Performance: 3307.113 tau/day, 3827.677 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0.00060225 | 0.00060934 | 0.00061345 |   0.0 |  0.02
Comm    | 0.029197   | 0.029376   | 0.029582   |   0.1 |  0.94
Output  | 0.00060606 | 0.00087148 | 0.0016448  |   0.0 |  0.03
Modify  | 2.84       | 2.8773     | 2.8942     |   1.3 | 91.78
Other   |            | 0.2269     |            |       |  7.24

Nlocal:        1024.00 ave        1037 max         999 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost:         0.00000 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Neighbor list builds = 73
Dangerous builds = 0

# if you want to check that rotational diffusion is behaving as expected,
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
# which should decay exponentially with timescale (d-1)*D_r (with d
# being simulation dimension)

#dump            1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type #               x y xu yu mux muy muz fx fy fz
#dump_modify     1 first yes sort id

#run             120000
Total wall time: 0:00:04
